zjyzjjzmt's repositories
lovis4u
Bioinformatics tool for Locus Visualisation
vamb
Variational autoencoder for metagenomic binning
RESCRIPt
REference Sequence annotation and CuRatIon Pipeline
Flye
De novo assembler for single molecule sequencing reads using repeat graphs
Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
YACHT
A mathematically characterized hypothesis test for organism presence/absence in a metagenome
cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
VIRIDIC
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes.
ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
RiverMethaneFlux
This is an ongoing project trying to quantify CH4 emissions from rivers in space and time.
run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
WMSA
The Multiple Sequence Alignment which developed by Wym6912
AncientMetagenomeDir
Repository containing lists of all published ancient metagenome samples (and related)
pilon
Pilon is an automated genome assembly improvement and variant detection tool
vRhyme
Binning Virus Genomes from Metagenomes
iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
serratus
Ultra-deep search for novel viruses
plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
MGV
Supporting code for uncultivated gut virus manuscript